run_PHATE_EB fails in Matlab2015a at line 73 in compute_alpha_kernel_sparse

[dxjones]

There is a bug on line 73 in computer_alpha_kernel_sparse.m

When I execute "run_phate_EB" it fails because the 2 operands of "./" are different sizes.

I think this could probably be corrected using "repmat", assuming that is what was intended.

I wonder if this line of code depends on a very recent feature in Matlab that does the "repmat" implicitly. Since many research lab run do not run the most up-to-date version of Matlab, it would be better to use repmat explicitly.

Here are more details:

>> run_phate_EB
PCA using random SVD
Elapsed time is 6.751585 seconds.
Doing PCA
PCA using random SVD
PCA took 8.1852 seconds
using alpha decaying kernel
Computing alpha decay kernel:
Number of samples = 16825
First iteration: k = 100
Error using  ./ 
Matrix dimensions must agree.

Error in compute_alpha_kernel_sparse (line 73)
    K=exp(-(kdist(idx_thresh,:)./epsilon(idx_thresh)).^a);

Error in phate (line 196)
        K = compute_alpha_kernel_sparse(pc, 'k', k, 'a', a, 'distfun', distfun);

Error in run_phate_EB (line 35)
Y_PHATE_2D = phate(data, 't', 20);

When I print out the "size" of the 2 operands, ... here is what I get:

>> size( exp( kdist(idx_thresh,:)) )
ans =

        9228         100

>> size( epsilon(idx_thresh) )
ans =

        9228           1

[dxjones]

Here is a one-line fix to resolve this error:

new line 73 in compute_alpha_kernel_sparse.m

    K=exp(-(kdist(idx_thresh,:)./repmat(epsilon(idx_thresh),1,size(kdist,2))).^a);

old:

    K=exp(-(kdist(idx_thresh,:)./epsilon(idx_thresh)).^a);

Similarly, another fix is required a few lines later:

new:

    K2=exp(-(kdist2(idx_thresh2,:)./repmat(epsilon2(idx_thresh2),1,size(kdist2,2))).^a);

old:

     K2=exp(-(kdist2(idx_thresh2,:)./epsilon2(idx_thresh2)).^a);

[dvdijk]

thanks for pointing out this issue. I have fixed it using your suggested code. Its currently on Dev branch but we'll merge to Master soon.

[scottgigante]

This issue was fixed in commit c39a40d